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   <TITLE>Violation check</TITLE>
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<H1><A HREF=".">Aqua server</A></H1>
<H2><A HREF="./viol_chk.html">
Violation check</A></H2>
<BR><BR>


<HR><FORM METHOD="POST"
ACTION="CGI_LOC/Aqua/viol_chk.pl" 
ENCTYPE="multipart/form-data">

<P>You need to supply both a restraint and a coordinate file.</P>

<P><B>NOE file:<INPUT 
TYPE="file"
NAME="NOE_FILE" 
VALUE=""
SIZE=50 ></B>

<P>The restraint file should be in the AQUA format described 
<A HREF="http://www.nmr.chem.uu.nl/users/rull/pcheck_dir/nmr_manual/manappb.html">here</A>.
You can use the <A HREF="brsvg.noe">example</A> restraint file (derived
from 
<A HREF="ftp://ftp.rcsb.org/pub/pdb/data/structures/all/nmr_restraints/1brv.mr.Z">
PDB mr file for 1BRV</A>).

<P>
Please use this <A HREF="qconvert.html">conversion server</A>
if you are unable to provide the AQUA formatted restraint file. 
</P>

<BR><B>PDB file:<INPUT 
TYPE="file" 
NAME="PDB_FILE" 
VALUE="" 
SIZE=50 ></B>

<P>
<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-pdb" CHECKED> PDB
<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-xplor"> XPLOR
<INPUT TYPE="radio" NAME="Pdb_type"
VALUE="-molmol"> MOLMOL
</P>

<P>The coordinate file should be in 
<A HREF="http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html">
PDB format</A>. You can use the <A HREF="brsvg.pdb">example</A> structure (first
2 models of PDB entry 
<A HREF="http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1BRV">1BRV</A>
). If you use an XPLOR or MOLMOL type of pdb file you can try selecting that
type.

<P><B>OPTIONS:</B>
<TABLE BORDER CELLSPACING=0 CELLPADDING=10 >
<TR>
<TD>

<DL>


<DT>
Use external atom names to match restraint atoms to coordinate atoms
(default is to use internal names):</DT>
<DD>
<INPUT TYPE="radio" NAME="External_match"
VALUE="true"                      >yes
<INPUT TYPE="radio" NAME="External_match"
VALUE="false"     CHECKED         >no</DD>

<DT>
Delete/combine similar restraints:</DT>
<DD>
<INPUT TYPE="radio" NAME="Multi_restraints"
VALUE="true"        CHECKED >yes
<INPUT TYPE="radio" NAME="Multi_restraints"
VALUE="false"               >no</DD>


<DT>
Type of averaging for all restraints:
<DD>
<INPUT TYPE="radio" NAME="Averaging_type"
VALUE="standard"        CHECKED >standard
<INPUT TYPE="radio" NAME="Averaging_type"
VALUE="r6ave"               >r<SUP>6</SUP>ave</DD>
<INPUT TYPE="radio" NAME="Averaging_type"
VALUE="r6sum"               >r<SUP>6</SUP>sum</DD>

<DT>
If averaging is set to r<SUP>6</SUP>sum in the previous section then supply 
the number of monomers n (1 <= n < 999) if larger than one:
<DD>
<INPUT TEXT NAME="Number_monomers" VALUE="1" size=2></DD>

<DT><A HREF="../html/terseness.html">Terseness</A> of the output (0[most verbose] through 9[default]):</DT>

<DD>
<INPUT TEXT NAME="Terseness" VALUE="9" size=2></DD>

</TR>
</TABLE>

<P><INPUT 
TYPE="submit" 
NAME="SUBMIT"
VALUE="Start uploading the Query!"></FORM>
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<P>Contact the 
<A HREF="mailto:jurgenfd@gmail.com">author</A> or 
<A HREF="mailto:WEBMASTER">webmaster</A>
for help, when required.
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